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Distance Maps
Below shows 3D Images of many proteins (copied from http://www.rcsb.org) along-side their corresponding Distance Maps (made at http://nanohub.org/resources/contactmaps using each protein's *.pdb file). Most proteins were chosen to represent different classes within the SCOPe database (http://scop.berkeley.edu). SCOPe classes a to j are natural proteins and peptides. Ones in class k are designed proteins. Each 3D Image below uses a color scheme in which low-numbered residues are blue while high-numbered residues are red. Some images come from NMR ensembles and so show multiple strands of the same protein with the same coloring but slightly different conformations. Each Distance Map below shows the Cα-Cα distance between every pair of amino acids in the protein as a two-dimensional matrix of shaded pixels. Dark pixels represent close pairs of residues. Light pixels represent distant pairs of residues. Low-numbered residues are in the lower left. High-numbered residues are in the upper right. Images labeled "Distance Map 1" show the 1st conformation from an NMR ensemble in which the same protein exists in multiple slightly-different conformations. If all the images below were scrambled, could you use your pattern-recognition skills to pick which ones went together? See http://memorize.com/protein-distance-maps to find out! =SCOPe Class a - All alpha proteins= 3QM9_bio_r_500.jpg|3QM9 (SCOPe Family a.1.1.2) 3QM9.jpg|3QM9 - Distance Map 2KK0_asym_r_500.jpg|2KK0 (SCOPe Family a.4.3.1) 2KK0-1of20.jpg|2KK0 - Distance Map 1 2KKO_asym_r_500.jpg|2KKO (SCOPe Family a.4.5.0) 2KKO-1of20.jpg|2KKO - Distance Map 1 1BAL_asym_r_500.jpg|1BAL (SCOPe Family a.9.1.1) 1BAL-1of56.jpg|1BAL - Distance Map 1 2LQI_asym_r_500.jpg|2LQI (SCOPe Family a.12.1.1) 2LQI-1of20.jpg|2LQI - Distance Map 1 1AUM_asym_r_500.jpg|1AUM (SCOPe Family a.28.3.1) 1AUM.jpg|1AUM - Distance Map 2EZW_asym_r_500.jpg|2EZW (SCOPe Family a.31.1.1) 2EZW-1of18.jpg|2EZW - Distance Map 1 3IM3_asym_r_500.jpg|3IM3 (SCOPe Family a.31.1.1) 3IM3.jpg|3IM3 - Distance Map 3IM4_bio_r_500.jpg|3IM4 (SCOPe Family a.31.1.1) 3IM4.jpg|3IM4 - Distance Map 2BCA_asym_r_500.jpg|2BCA (SCOPe Family a.39.1.1) 2BCA.jpg|2BCA - Distance Map 1BR4_asym_r_500.jpg|1BR4 (SCOPe Families a.39.1.5, b.34.3.1, & c.37.1.9) 1BR4.jpg|1BR4 - Distance Map 3NFT_asym_r_500.jpg|3NFT (SCOPe Family a.250.1.1) 3NFT.jpg|3NFT - Distance Map 2QVJ_asym_r_500.jpg|2QVJ (SCOPe Family a.260.1.1) 2QVJ.jpg|2QVJ - Distance Map Back to Top =SCOPe Class b - All beta proteins= 1A7O_bio_r_500.jpg|1A7O (SCOPe Family b.1.1.1) 1A7O.jpg|1A7O - Distance Map 1B4R_asym_r_500.jpg|1B4R (SCOPe Family b.1.3.1) 1B4R-1of20.jpg|1B4R - Distance Map 1 2JNZ_asym_r_500.jpg|2JNZ (SCOPe Family b.7.3.0) 2JNZ-1of20.jpg|2JNZ - Distance Map 1 3FT1_asym_r_500.jpg|3FT1 (SCOPe Family b.7.3.0) 3FT1.jpg|3FT1 - Distance Map 1BR4_asym_r_500.jpg|1BR4 (SCOPe Families a.39.1.5, b.34.3.1, & c.37.1.9) 1BR4.jpg|1BR4 - Distance Map 2L15_asym_r_500.jpg|2L15 (SCOPe Family b.40.4.5) 2L15-1of10.jpg|2L15 - Distance Map 1 1DC9_bio_r_500.jpg|1DC9 (SCOPe Family b.60.1.12) 1DC9.jpg|1DC9 - Distance Map 2HO2_bio_r_500.jpg|2HO2 (SCOPe Family b.72.1.1) 2HO2.jpg|2HO2 - Distance Map 1UCS_bio_r_500.jpg|1UCS (SCOPe Family b.85.1.1) 1UCS.jpg|1UCS - Distance Map 4AKM_asym_r_500.jpg|4AKM (SCOPe Family b.180.1.1) 4AKM.jpg|4AKM - Distance Map 4E0E_asym_r_500.jpg|4E0E (SCOPe Family ?) 4E0E.jpg|4E0E - Distance Map Back to Top =SCOPe Class c - Alpha and beta proteins (a/b)= 1H16_asym_r_500.jpg|1H16 (SCOPe Family c.7.1.1) 1H16.jpg|1H16 - Distance Map 1LA1_bio_r_500.jpg|1LA1 (SCOPe Family c.8.5.1) 1LA1.jpg|1LA1 - Distance Map 1BR4_asym_r_500.jpg|1BR4 (SCOPe Families a.39.1.5, b.34.3.1, & c.37.1.9) 1BR4.jpg|1BR4 - Distance Map 2HSH_bio_r_500.jpg|2HSH (SCOPe Family c.47.1.1) 2HSH.jpg|2HSH - Distance Map 1WOU_bio_r_500.jpg|1WOU (SCOPe Family c.47.1.16) 1WOU.jpg|1WOU - Distance Map 4R5F_asym_r_500.jpg|4R5F (SCOPe Family c.67.1.0) 4R5F.jpg|4R5F - Distance Map 4EB5_bio_r_500.jpg|4EB5 (SCOPe Families c.67.1.0 & d.224.1.0) 4EB5 Distance Map.jpg|4EB5 - Distance Map 4EB7_bio_r_500.jpg|4EB7 (SCOPe Families c.67.1.0 & d.224.1.0) 4EB7.jpg|4EB7 - Distance Map 4KT7_bio_r_500.jpg|4KT7 (SCOPe Family c.68.1.0) 4KT7distmap.jpg|4KT7 - Distance Map 2ZWI_asym_r_500.jpg|2ZWI (SCOPe Family c.87.1.0) 2ZWI.jpg|2ZWI - Distance Map 3DNF_bio_r_500.jpg|3DNF (SCOPe Family c.155.1.1) 3DNF.jpg|3DNF - Distance Map Back to Top =SCOPe Class d - Alpha and beta proteins (a+b)= 135L_bio_r_500.jpg|135L (SCOPe Family d.2.1.2) 135L.jpg|135L - Distance Map 2VB1_bio_r_500.jpg|2VB1 (SCOPe Family d.2.1.2) 2VB1.jpg|2VB1 - Distance Map 2FHT_bio_r_500.jpg|2FHT (SCOPe Family d.9.1.1) 2FHT.jpg|2FHT - Distance Map 1BB8_asym_r_500.jpg|1BB8 (SCOPe Family d.10.1.1) 1BB8-1of25.jpg|1BB8 - Distance Map 1 2LI5_asym_r_500.jpg|2LI5 (SCOPe Family d.15.1.3) 2LI5-1of19.jpg|2LI5 - Distance Map 1 1A70_bio_r_500.jpg|1A70 (SCOPe Family d.15.4.1) 1A70.jpg|1A70 - Distance Map 2ZW1_bio_r_500.jpg|2ZW1 (SCOPe Family d.15.7.1) 2ZW1.jpg|2ZW1 - Distance Map 3E8P_bio_r_500.jpg|3E8P (SCOPe Family d.38.1.0) 3E8P.jpg|3E8P - Distance Map 1VEH_asym_r_500.jpg|1VEH (SCOPe Family d.52.8.1) 1VEH-1of20.jpg|1VEH - Distance Map 1 3S7R_asym_r_500.jpg|3S7R (SCOPe Family d.58.7.1) 3S7R.jpg|3S7R - Distance Map 2L3M_asym_r_500.jpg|2L3M (SCOPe Family d.58.17.0) 2L3M Distance Map.jpg|2L3M - Distance Map 1CPZ_asym_r_500.jpg|1CPZ (SCOPe Family d.58.17.1) 1CPZ-1of20.jpg|1CPZ - Distance Map 1 1KP6_bio_r_500.jpg|1KP6 (SCOPe Family d.58.25.1) 1KP6 - Distance Map.jpg|1KP6 - Distance Map 4GVB_bio_r_500.jpg|4GVB (SCOPe Family d.58.25.1) 4GVB.jpg|4GVB - Distance Map 3EPU_asym_r_500.jpg|3EPU (SCOPe Family d.198.1.0) 3EPU.jpg|3EPU - Distance Map 2QQ4_asym_r_500.jpg|2QQ4 (SCOPe Family d.224.1.0) 2QQ4.jpg|2QQ4 - Distance Map 2Z7E_asym_r_500.jpg|2Z7E (SCOPe Family d.224.1.0) 2Z7E.jpg|2Z7E - Distance Map 4EB5_bio_r_500.jpg|4EB5 (SCOPe Families c.67.1.0 & d.224.1.0) 4EB5 Distance Map.jpg|4EB5 - Distance Map 4EB7_bio_r_500.jpg|4EB7 (SCOPe Families c.67.1.0 & d.224.1.0) 4EB7.jpg|4EB7 - Distance Map 4EOE_bio_r_500.jpg|4EOE (SCOPe Family d.248.2.1) 4EOE.jpg|4EOE - Distance Map 3FKE_asym_r_500.jpg|3FKE (SCOPe Family d.388.1.1) 3FKE.jpg|3FKE - Distance Map Back to Top =SCOPe Class e - Multi-domain proteins (alpha and beta)= 2P74_asym_r_500.jpg|2P74 (SCOPe Family e.3.1.1) 2P74.jpg|2P74 - Distance Map 3M4I_asym_r_500.jpg|3M4I (SCOPe Family e.78.1.1) 3M4I.jpg|3M4I - Distance Map Back to Top =SCOPe Class f - Membrane and cell surface proteins and peptides= 3SP7_bio_r_500.jpg|3SP7 (SCOPe Family f.1.4.1) 3SP7.jpg|3SP7 - Distance Map 4AL0_asym_r_500.jpg|4AL0 (SCOPe Family f.56.1.0) 4AL0.jpg|4AL0 - Distance Map Back to Top =SCOPe Class g - Small proteins= 1BCG_asym_r_500.jpg|1BCG (SCOPe Family g.3.7.1) 1BCG.jpg|1BCG - Distance Map 1CCM_asym_r_500.jpg|1CCM (SCOPe Family g.13.1.1) 1CCM-1of8.jpg|1CCM - Distance Map 1 3NIR_bio_r_500.jpg|3NIR (SCOPe Family g.13.1.1) 3NIR.jpg|3NIR - Distance Map 1RO3_asym_r_500.jpg|1RO3 (SCOPe Family g.20.1.1) 1RO3-1of20.jpg|1RO3 - Distance Map 1 2ECH_asym_r_500.jpg|2ECH (SCOPe Family g.20.1.1) 2ECH-1of8.jpg|2ECH - Distance Map 1 2P8Q_bio_r_500.jpg|2P8Q (SCOPe Family g.88.2.1) 2P8Q.jpg|2P8Q - Distance Map Back to Top =SCOPe Class h - Coiled coil proteins= 1P9I_asym_r_500.jpg|1P9I (SCOPe Family h.1.10.1) 1P9I.jpg|1P9I - Distance Map 4M44_bio_r_500.jpg|4M44 (SCOPe Family h.3.1.1) 4M44.jpg|4M44 - Distance Map 1AV1_bio_r_500.jpg|1AV1 (SCOPe Family h.5.1.1) 1AV1.jpg|1AV1 - Distance Map 1K4R_asym_r_500.jpg|1K4R 1K4R.jpg|1K4R - Distance Map 1DY1_bio_r_500.jpg|1DY1 1DY1.jpg|1DY1 - Distance Map Back to Top =SCOPe Class i - Low resolution protein structures= 1QO1_bio_r_500.jpg|1QO1 (SCOPe Family i.3.1.1) 1QO1.jpg|1QO1 - Distance Map 1MHS_bio_r_500.jpg|1MHS (SCOPe Family i.18.1.1) 1MHS.jpg|1MHS - Distance Map 4A10_bio_r_500.jpg|4A10 (SCOPe Family ?) 4A10.jpg|4A10 - Distance Map Back to Top =SCOPe Class j - Peptides= 1TK2_bio_r_500.jpg|1TK2 (SCOPe Family j.1.1.1) 1TK2.jpg|1TK2 - Distance Map 1JFW_asym_r_500.jpg|1JFW (SCOPe Family j.9.4.1) 1JFW-1of11.jpg|1JFW - Distance Map 1 1TER_asym_r_500.jpg|1TER (SCOPe Family j.20.1.1) 1TER-1of21.jpg|1TER - Distance Map 1 1EDN_asym_r_500.jpg|1EDN (SCOPe Family j.28.1.1) 1EDN.jpg|1EDN - Distance Map 1SUT_asym_r_500.jpg|1SUT (SCOPe Family j.41.1.1) 1SUT-1of10.jpg|1SUT - Distance Map 1 1Q2F_asym_r_500.jpg|1Q2F (SCOPe Family j.69.1.1) 1Q2F-1of30.jpg|1Q2F - Distance Map 1 1EI0_asym_r_500.jpg|1EI0 (SCOPe Family j.77.1.1) 1EI0.jpg|1EI0 - Distance Map 1OEI_asym_r_500.jpg|1OEI (SCOPe Family j.90.1.1) 1OEI-1of20.jpg|1OEI - Distance Map 1 1LVQ_asym_r_500.jpg|1LVQ (SCOPe Family j.101.1.1) 1LVQ.jpg|1LVQ - Distance Map 1LVR_asym_r_500.jpg|1LVR (SCOPe Family j.101.1.1) 1LVR.jpg|1LVR - Distance Map Back to Top =SCOPe Class k - Designed proteins= 1CIS_asym_r_500.jpg|1CIS (SCOPe Family k.1.1.1) 1CIS-1of15.jpg|1CIS - Distance Map 1 1VRZ_asym_r_500.jpg|1VRZ (SCOPe Family k.15.1.1) 1VRZ.jpg|1VRZ - Distance Map 1QUZ_asym_r_500.jpg|1QUZ (SCOPe Family k.23.1.1) 1QUZ-1of20.jpg|1QUZ - Distance Map 1 2FCS_asym_r_500.jpg|2FCS (SCOPe Family k.45.1.1) 2FCS.jpg|2FCS - Distance Map 2CW1_asym_r_500.jpg|2CW1 (SCOPe Family k.46.1.1) 2CW1-1of10.jpg|2CW1 - Distance Map 1 Back to Top If all the images above were scrambled, could you use your pattern-recognition skills to pick which ones went together? See http://memorize.com/protein-distance-maps to find out! =References= (1) To make Distance Maps like above, see: Benjamin Rafferty; Zachary Carl Flohr; Ashlie Martini (2014), "Protein Contact Maps", http://nanohub.org/resources/contactmaps (http://dx.doi.org/10.4231/D35M62761). (2) For more details about any protein above, use its PDB ID (for example, 2QQ4) in the following: http://www.rcsb.org/pdb/explore/explore.do?structureId=2QQ4 http://scop.berkeley.edu/search/?ver=2.05&key=2QQ4 (3) For more details about any SCOPe family above, use its code (for example, d.224.1.0) in the following: http://scop.berkeley.edu/search/?ver=2.05&key=d.224.1.0